Unlike the other prominent young quarterbacks around the league, Kaepernick — along with Russell Wilson and Andy Dalton — was not a high draft pick, selected by a struggling team in need of a savior. Instead, Kaepernick was plugged into the starting lineup of a talented 6-2 team coming off an overtime loss in the NFC Championship Game the previous season.

Kaepernick has put up good passing numbers and he is one of the most dangerous quarterbacks when he gets outside of the pocket. But can he replicate that success without the immense talent he has surrounding him in San Francisco?

If he is going to take up nearly a sixth of the team’s cap room, Kaepernick will have to shoulder more of a load than he’s had to in his first two years as a starter. With $13 million in cap room, the 49ers are in decent shape cap-wise, but Frank Gore, Michael Crabtree, Mike Iupati, Aldon Smith, Vernon Davis and Justin Smith will all be free agents in the next two years, according to Spotrac.

In Alex Smith’s two seasons under Niners coach Jim Harbaugh, he put up similar passing statistics as Kaepernick, without the running contributions. But Smith is being paid less than half of what Kaepernick is reportedly asking for. And if the 49ers are going to commit long-term money, protecting that investment would likely include cutting back on Kaepernick’s scrambling even more than they did in 2013.

Take away Kaepernick’s legs and what do you have? The 26-year-old has all the physical tools teams look for in a passer. He’s big, strong, mobile and his accuracy improved as the season went on.

The one thing lacking in Kaepernick’s game is pocket presence. At this point in his career, he is not comfortable in the pocket. Despite Kaepernick’s running ability, he’s not very good at handling pressure — perceived or otherwise.

Kaepernick scrambled on 16.6 percent of his unpressured dropbacks — the highest percentage in the league by a wide margin — instead of hanging in the pocket and working through his progressions. When he was pressured, Kaepernick completed just 43.6 percent of his passes and was sacked on 20 percent of those dropbacks, fifth most in the league, according to Pro Football Focus.

The 49ers are in a tough spot. They can’t afford to let a star quarterback leave in free agency, but it’s likely going to take a $100 million bet to prevent that scenario from happening. If San Francisco pays Kaepernick, and he doesn’t improve in the pocket, their window as Super Bowl contenders will be closed for the duration of the deal.